Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues

Sinem K Saka; Yu Wang; Jocelyn Y Kishi; Allen Zhu; Yitian Zeng; Wenxin Xie; Koray Kirli; Clarence Yapp; Marcelo Cicconet; Brian J Beliveau; Sylvain W Lapan; Siyuan Yin; Millicent Lin; Edward S Boyden; Pascal S Kaeser; German Pihan; George M Church; Peng Yin

doi:10.1038/s41587-019-0207-y

Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues

Nat Biotechnol. 2019 Sep;37(9):1080-1090. doi: 10.1038/s41587-019-0207-y. Epub 2019 Aug 19.

Authors

Sinem K Saka^#^{1

2}, Yu Wang^#^{3

4

5}, Jocelyn Y Kishi^{6

7}, Allen Zhu^{6

7}, Yitian Zeng^{6

8}, Wenxin Xie^{6

8}, Koray Kirli⁹, Clarence Yapp^{10

11}, Marcelo Cicconet¹⁰, Brian J Beliveau^{6

7

12}, Sylvain W Lapan⁸, Siyuan Yin^{6

8}, Millicent Lin^{6

8}, Edward S Boyden¹³, Pascal S Kaeser¹⁴, German Pihan¹⁵, George M Church^{6

8}, Peng Yin^{16

17}

Affiliations

¹ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. sinem.saka@wyss.harvard.edu.
² Department of Systems Biology, Harvard Medical School, Boston, MA, USA. sinem.saka@wyss.harvard.edu.
³ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. yuwang01@fas.harvard.edu.
⁴ Department of Systems Biology, Harvard Medical School, Boston, MA, USA. yuwang01@fas.harvard.edu.
⁵ Department of Genetics, Harvard Medical School, Boston, MA, USA. yuwang01@fas.harvard.edu.
⁶ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
⁷ Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
⁸ Department of Genetics, Harvard Medical School, Boston, MA, USA.
⁹ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
¹⁰ Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA.
¹¹ Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
¹² Department of Genome Sciences, University of Washington, Seattle, WA, USA.
¹³ Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.
¹⁴ Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
¹⁵ Pathology Department, Beth Israel Deaconess Medical Center, Boston, MA, USA.
¹⁶ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. py@hms.harvard.edu.
¹⁷ Department of Systems Biology, Harvard Medical School, Boston, MA, USA. py@hms.harvard.edu.

^# Contributed equally.

Abstract

Spatial mapping of proteins in tissues is hindered by limitations in multiplexing, sensitivity and throughput. Here we report immunostaining with signal amplification by exchange reaction (Immuno-SABER), which achieves highly multiplexed signal amplification via DNA-barcoded antibodies and orthogonal DNA concatemers generated by primer exchange reaction (PER). SABER offers independently programmable signal amplification without in situ enzymatic reactions, and intrinsic scalability to rapidly amplify and visualize a large number of targets when combined with fast exchange cycles of fluorescent imager strands. We demonstrate 5- to 180-fold signal amplification in diverse samples (cultured cells, cryosections, formalin-fixed paraffin-embedded sections and whole-mount tissues), as well as simultaneous signal amplification for ten different proteins using standard equipment and workflows. We also combined SABER with expansion microscopy to enable rapid, multiplexed super-resolution tissue imaging. Immuno-SABER presents an effective and accessible platform for multiplexed and amplified imaging of proteins with high sensitivity and throughput.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Antibodies / immunology*
Antibodies / metabolism*
Cell Line
DNA / analysis
DNA Barcoding, Taxonomic
Fluorescent Dyes
Humans
Immunohistochemistry / methods*
In Situ Hybridization, Fluorescence / methods
Mice
Microscopy, Fluorescence / methods
Proteins / metabolism*
Retina / cytology
Staining and Labeling*

Substances

Antibodies
Fluorescent Dyes
Proteins
DNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding